Daniel:Notebook/Haplotyping: Difference between revisions

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{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
|- style="font-size:12pt" align="center" valign="bottom"
|- style="font-size:12pt" align="center" valign="bottom"
|align="center" width="500" | Aim
|align="center" width="500" | '''Specific Aim'''
|align="center" width="65" | Date to Completion
|align="center" width="65" | Date to Completion
|align="center" width="65" | Date of Completion
|align="center" width="65" | Date of Completion
|align="center" width="150" | Link to posted data
|align="center" width="250" | Notebook Link


|- style="font-size:12pt" align="center" valign="bottom"
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | Concordance tables comparing SISSOR, BAC, and HiC data
| height="15" align="left" | Combine PGP1 data from Complete Genomics WGS to create more defendable/accurate VCF
| align="center" | January 1, 2015
| align="center" | January 1, 2016
| align="center" |  
| align="center" |  
| align="center" | [[Daniel:Notebook/Haplotyping/MergeVCF|Merging Complete Genomics WGS data]]
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" align="left" | Comparing data sets using consistent pairs method
| align="center" | January 1, 2016
| align="center" |  
| align="center" |  
| align="center" | [[Daniel:Notebook/Haplotyping/ConsistentPairs|Consistent Pairs Method]]
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" align="left" | Use BEAGLE to get inferences for PGP1
| align="center" | August 1, 2015
| align="center" |
| align="center" | [[Daniel:Notebook/Haplotyping/BEAGLE|Using BEAGLE to infer population data]]
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" align="left" | Assess variant calling using freebayes, create ROC
| align="center" | January 1, 2016
| align="center" |
| align="center" |  [[Danie:Notebook/Haplotyping/Genotyping|Genotyping Samples]]
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" align="left"| Combine Hi-C and BAC data to get more complete haplotypes
| align="center" | August 1, 2015
| align="center" |
| align="center" | [[Daniel:Notebook/Haplotyping/HiCBAC|Combining BAC and HiC Data]]


|- style="font-size:12pt" align="center" valign="bottom"
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | Use BEAGLE to get inferences for PGP1
| height="15" align="left" | Use Eric's pipeline to segment SISSOR data
| align="center" | January 1, 2015
| align="center" | January 1, 2015
| align="center" |
| align="center" |  
| align="center" |
| align="center" | [[Daniel:Notebook/Haplotyping/SISSORPipeline|SISSOR Segmentation Pipeline]]


|- style="font-size:12pt" align="center" valign="bottom"
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" | Combine Hi-C and BAC data to get more complete haplotypes
| height="15" align="left" | Compare haplotypes in MHC Region
| align="center" | January 1, 2015
| align="center" | January 1, 2015
| align="center" |
| align="center" |  
| align="center" |
| align="center" |  
 
|- style="font-size:12pt" align="center" valign="bottom"
| height="15" align="left" | CPT-Seq for PGP1
| align="center" | March 1, 2016
| align="center" |
| align="center" | [[Daniel:Notebook/Haplotyping/CPTSeq-PGP1|CPT-Seq Pipeline]]


|}
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*[[Daniel:Notebook/Haplotyping/Pipeline|Analysis Pipelines]]
*[[Daniel:Notebook/Haplotyping/Pipeline|Analysis Pipelines]]


==Calendar==
==Calendar and Experiments==
 
==CPT-Seq for PGP1==
 
[[Daniel:Notebook/Haplotyping/2016-1-31|High MW DNA Extraction]]


<calendar>
<calendar>

Latest revision as of 21:52, 14 February 2016

Haplotyping Project[edit]

Back to Notebook

Experiment List

Aims[edit]

Overall aims for the paper, to be completed before publication

  • Compare BEAGLE computational inferences to experimental results
  • Create most complete diploid genome yet
  • Consensus results against published LFR data
  • Suggest the most cost effective way to phase a genome, including scale-up
  • Phase the HLA region with and without BEAGLE
    • Propose the most cost effective way to obtain this information on a per patient level

Specific Aims[edit]

Table of current specific aims, to be completed within short time frames. Specific aims should make progress towards the completion of aims (above).

Specific Aim Date to Completion Date of Completion Notebook Link
Combine PGP1 data from Complete Genomics WGS to create more defendable/accurate VCF January 1, 2016 Merging Complete Genomics WGS data
Comparing data sets using consistent pairs method January 1, 2016 Consistent Pairs Method
Use BEAGLE to get inferences for PGP1 August 1, 2015 Using BEAGLE to infer population data
Assess variant calling using freebayes, create ROC January 1, 2016 Genotyping Samples
Combine Hi-C and BAC data to get more complete haplotypes August 1, 2015 Combining BAC and HiC Data
Use Eric's pipeline to segment SISSOR data January 1, 2015 SISSOR Segmentation Pipeline
Compare haplotypes in MHC Region January 1, 2015
CPT-Seq for PGP1 March 1, 2016 CPT-Seq Pipeline

Data[edit]

List of pages related to data.

Calendar and Experiments[edit]

CPT-Seq for PGP1[edit]

High MW DNA Extraction

<calendar> name=Daniel:Notebook/Haplotyping format=%name/%year-%month-%day date=2014/02/01 view=oneyear </calendar>

Data[edit]

Athurva's GATK Pipeline for Variant Calling

This project utilizes several data sources. The data sources and relevant information are listed below.

BAC Data[edit]

The BAC data is on genome miner, in the following path:

  • /media/LTS_33T/KZ_LTS33T/PGP1_BacPool

The folder contains several subfolders:

  • old_calls
    • Contains the old variant call files
  • vcf_files
    • Contains a lot of vcf files
  • all_pools_combined
    • Contains all the heterozygous call files. Still unsure of the format
  • fixed.bam
    • Contains all of the bam files for each index
  • filtered_vcf
    • Seems to contain the newest .vcf files, probably the best ones to use
  • assembled_haplotypes
    • Contains the final phase output of HapCUT that was used for the BAC pools
  • het_sites
    • Contains the heterozygous site files for each chromosome. Still unsure of the format

HiC Data[edit]

The HiC data is on TSCC, in the following path:

  • /oasis/tscc/scratch/sselvaraj/human_tissues/htissues/KZPGP1/fastq/hi-c

Microfluidic Data[edit]

The data sets are on genome miner, in the following paths:

  • Better one:/media/Syn_15T/Eric_15T/PGP1_21
  • Second best:/media/Syn_15T/Eric_15T/PGP1_22

This data may have to be processed in the same manner as the BAC pools. If so, I will follow Athurva's pipeline, which was used for the original BAC pool paper.